Loading the library
library(Seurat)
Setting the working directory
setwd("C:/Users/savill/OneDrive/Documents/PhD Jesse/R-Objects")
Loading the data
# load my data
Gastruloid_48h_merged_afterQC <- readRDS("./df48v3.rds")
DefaultAssay(Gastruloid_48h_merged_afterQC) <- "RNA"
Gastruloid_48h_merged_afterQC <- SetIdent(Gastruloid_48h_merged_afterQC, value = "predicted.id")
Getting the metadata and taking a peak:
metadata <- Gastruloid_48h_merged_afterQC@meta.data
head(metadata)
Get all the columns so we can delete the old morphology info:
colnames(metadata)
[1] "orig.ident" "nCount_RNA" "nFeature_RNA" "Sample.barcode" "Morphotype" "percent.mt" "RNA_snn_res.0.4"
[8] "seurat_clusters" "S.Score" "G2M.Score" "Phase" "old.ident" "RNA_snn_res.0.2" "Area"
[15] "AR" "percent.ribo" "RNA_snn_res.0.3" "RNA_snn_res.0.1" "RNA_snn_res.0.25" "RNA_snn_res.0.35" "RNA_snn_res.0.5"
[22] "RNA_snn_res.0.6" "hippopath1" "hippopath2" "hippopath3" "hippopath4" "hippopath5" "hippopath6"
[29] "hippopath7" "hippopath8" "hippopath9" "hippopath10" "hippopath11" "hippopath12" "hippopath13"
[36] "hippopath14" "hippopath15" "hippopath16" "hippopath17" "hippopath18" "hippopath19" "hippo1"
[43] "hippo2" "hippo3" "hippo4" "hippo5" "hippo6" "hippo7" "hippo8"
[50] "hippo9" "hippo10" "hippo11" "hippo12" "hippo13" "hippo14" "hippo15"
[57] "hippo16" "hippo17" "hippo18" "hippo19" "Cluster1" "Cluster21" "Cluster22"
[64] "Cluster23" "Cluster24" "Cluster25" "Cluster26" "Cluster27" "Cluster28" "Cluster29"
[71] "Cluster210" "Cluster211" "Cluster212" "Cluster213" "Cluster214" "Cluster215" "Cluster216"
[78] "Cluster217" "Cluster218" "Cluster219" "Cluster2" "Cluster3" "Cluster4" "Cluster5"
[85] "Cluster6" "Cluster7" "Cluster8" "Cluster9" "Cluster10" "Cluster11" "Cluster12"
[92] "Cluster13" "Cluster14" "Cluster15" "Cluster16" "Cluster17" "Cluster18" "Cluster19"
all_features = colnames(metadata)
old_morpho_features = c("Area","AR")
metadata_old_removed = metadata[!(all_features %in% old_morpho_features)]
#index_name = "row_names"
#metadata_old_removed[, index_name] <- rownames(metadata_old_removed)
metadata_old_removed
NA
Now we can move on to loading the new features and adding them to the metadata:
my_data_48h = read.csv("Morphodata_All_Features_Sequenced_048h.csv")
dim(my_data_48h)
[1] 72 537
my_data_48h
Adding the identifier so we can merge the dataframes:
# if this is how we add the barcode identifyer it is CRITICAL that the order is the same as in the spreadsheet
# This means A1-A12 INSTEAD of A10,A11,A12,A1,A2 (which is the default order in python and pandas)
barcoder_identifier = "bar"
my_data_48h[barcoder_identifier] <- paste("Bar", c(1:72), sep="")
my_data_48h
Here I am basically excluding the columns we don’t want to add, assuming that we want to add all columns that are in the .csv file. Alternatively we could specify which columns (or which features) we want to add to the seurat object manually. No matter which way it is done we would have to add the sample barcode to be able to merge the data with the existing metadata.
all_columns = colnames(my_data_48h)
columns_we_dont_need = c('Sample','Multi_BC','Multi_BC_.','Morphotype',barcoder_identifier)
columns_we_need = all_columns[!(all_columns %in% columns_we_dont_need)]
for (feature_name in columns_we_need) {
metadata_old_removed[feature_name]<- my_data_48h[[feature_name]][match(metadata_old_removed$Sample.barcode, my_data_48h[[barcoder_identifier]])]
}
metadata_old_removed
actually adding the metadata to the Seurat object. One thing to do beforehand is removing the old morpho data from the seurat object
for (x in old_morpho_features) {
Gastruloid_48h_merged_afterQC@meta.data[[x]]=NULL
}
head(Gastruloid_48h_merged_afterQC@meta.data)
Now we can add the new metadata
for (feature_name in columns_we_need){
Gastruloid_48h_merged_afterQC <- AddMetaData(object = Gastruloid_48h_merged_afterQC, metadata = metadata_old_removed[[feature_name]], col.name = feature_name)
}
# Now we can look at the final dataframe:
Gastruloid_48h_merged_afterQC@meta.data
checking the column_names
colnames(Gastruloid_48h_merged_afterQC@meta.data)
[1] "orig.ident" "nCount_RNA"
[3] "nFeature_RNA" "Sample.barcode"
[5] "Morphotype" "percent.mt"
[7] "RNA_snn_res.0.4" "seurat_clusters"
[9] "S.Score" "G2M.Score"
[11] "Phase" "old.ident"
[13] "RNA_snn_res.0.2" "percent.ribo"
[15] "RNA_snn_res.0.3" "RNA_snn_res.0.1"
[17] "RNA_snn_res.0.25" "RNA_snn_res.0.35"
[19] "RNA_snn_res.0.5" "RNA_snn_res.0.6"
[21] "hippopath1" "hippopath2"
[23] "hippopath3" "hippopath4"
[25] "hippopath5" "hippopath6"
[27] "hippopath7" "hippopath8"
[29] "hippopath9" "hippopath10"
[31] "hippopath11" "hippopath12"
[33] "hippopath13" "hippopath14"
[35] "hippopath15" "hippopath16"
[37] "hippopath17" "hippopath18"
[39] "hippopath19" "hippo1"
[41] "hippo2" "hippo3"
[43] "hippo4" "hippo5"
[45] "hippo6" "hippo7"
[47] "hippo8" "hippo9"
[49] "hippo10" "hippo11"
[51] "hippo12" "hippo13"
[53] "hippo14" "hippo15"
[55] "hippo16" "hippo17"
[57] "hippo18" "hippo19"
[59] "Cluster1" "Cluster21"
[61] "Cluster22" "Cluster23"
[63] "Cluster24" "Cluster25"
[65] "Cluster26" "Cluster27"
[67] "Cluster28" "Cluster29"
[69] "Cluster210" "Cluster211"
[71] "Cluster212" "Cluster213"
[73] "Cluster214" "Cluster215"
[75] "Cluster216" "Cluster217"
[77] "Cluster218" "Cluster219"
[79] "Cluster2" "Cluster3"
[81] "Cluster4" "Cluster5"
[83] "Cluster6" "Cluster7"
[85] "Cluster8" "Cluster9"
[87] "Cluster10" "Cluster11"
[89] "Cluster12" "Cluster13"
[91] "Cluster14" "Cluster15"
[93] "Cluster16" "Cluster17"
[95] "Cluster18" "Cluster19"
[97] "Plate" "X048h_raw_BF_AreaShape_area"
[99] "X048h_raw_BF_AreaShape_aspect_ratio" "X048h_raw_BF_AreaShape_axis_major_length"
[101] "X048h_raw_BF_AreaShape_axis_minor_length" "X048h_raw_BF_AreaShape_eccentricity"
[103] "X048h_raw_BF_AreaShape_feret_diameter_max" "X048h_raw_BF_AreaShape_perimeter"
[105] "X048h_raw_BF_AreaShape_solidity" "X048h_str_BF_AreaShape_area"
[107] "X048h_str_BF_AreaShape_aspect_ratio" "X048h_str_BF_AreaShape_eccentricity"
[109] "X048h_str_BF_AreaShape_equivalent_diameter" "X048h_str_BF_AreaShape_extent"
[111] "X048h_str_BF_AreaShape_form_factor" "X048h_str_BF_AreaShape_inertia_tensor_0_0"
[113] "X048h_str_BF_AreaShape_inertia_tensor_0_1" "X048h_str_BF_AreaShape_inertia_tensor_1_0"
[115] "X048h_str_BF_AreaShape_inertia_tensor_1_1" "X048h_str_BF_AreaShape_inertia_tensor_eigvals_0"
[117] "X048h_str_BF_AreaShape_inertia_tensor_eigvals_1" "X048h_str_BF_AreaShape_locoefa_PC_1"
[119] "X048h_str_BF_AreaShape_locoefa_PC_2" "X048h_str_BF_AreaShape_locoefa_PC_3"
[121] "X048h_str_BF_AreaShape_locoefa_PC_4" "X048h_str_BF_AreaShape_locoefa_PC_5"
[123] "X048h_str_BF_AreaShape_locoefa_UMAP_1" "X048h_str_BF_AreaShape_locoefa_UMAP_2"
[125] "X048h_str_BF_AreaShape_locoefa_UMAP_3" "X048h_str_BF_AreaShape_locoefa_coeff_0"
[127] "X048h_str_BF_AreaShape_locoefa_coeff_1" "X048h_str_BF_AreaShape_locoefa_coeff_10"
[129] "X048h_str_BF_AreaShape_locoefa_coeff_11" "X048h_str_BF_AreaShape_locoefa_coeff_12"
[131] "X048h_str_BF_AreaShape_locoefa_coeff_13" "X048h_str_BF_AreaShape_locoefa_coeff_14"
[133] "X048h_str_BF_AreaShape_locoefa_coeff_15" "X048h_str_BF_AreaShape_locoefa_coeff_16"
[135] "X048h_str_BF_AreaShape_locoefa_coeff_17" "X048h_str_BF_AreaShape_locoefa_coeff_18"
[137] "X048h_str_BF_AreaShape_locoefa_coeff_19" "X048h_str_BF_AreaShape_locoefa_coeff_2"
[139] "X048h_str_BF_AreaShape_locoefa_coeff_20" "X048h_str_BF_AreaShape_locoefa_coeff_21"
[141] "X048h_str_BF_AreaShape_locoefa_coeff_22" "X048h_str_BF_AreaShape_locoefa_coeff_23"
[143] "X048h_str_BF_AreaShape_locoefa_coeff_24" "X048h_str_BF_AreaShape_locoefa_coeff_25"
[145] "X048h_str_BF_AreaShape_locoefa_coeff_26" "X048h_str_BF_AreaShape_locoefa_coeff_27"
[147] "X048h_str_BF_AreaShape_locoefa_coeff_28" "X048h_str_BF_AreaShape_locoefa_coeff_29"
[149] "X048h_str_BF_AreaShape_locoefa_coeff_3" "X048h_str_BF_AreaShape_locoefa_coeff_30"
[151] "X048h_str_BF_AreaShape_locoefa_coeff_31" "X048h_str_BF_AreaShape_locoefa_coeff_32"
[153] "X048h_str_BF_AreaShape_locoefa_coeff_33" "X048h_str_BF_AreaShape_locoefa_coeff_34"
[155] "X048h_str_BF_AreaShape_locoefa_coeff_35" "X048h_str_BF_AreaShape_locoefa_coeff_36"
[157] "X048h_str_BF_AreaShape_locoefa_coeff_37" "X048h_str_BF_AreaShape_locoefa_coeff_38"
[159] "X048h_str_BF_AreaShape_locoefa_coeff_39" "X048h_str_BF_AreaShape_locoefa_coeff_4"
[161] "X048h_str_BF_AreaShape_locoefa_coeff_40" "X048h_str_BF_AreaShape_locoefa_coeff_41"
[163] "X048h_str_BF_AreaShape_locoefa_coeff_42" "X048h_str_BF_AreaShape_locoefa_coeff_43"
[165] "X048h_str_BF_AreaShape_locoefa_coeff_44" "X048h_str_BF_AreaShape_locoefa_coeff_45"
[167] "X048h_str_BF_AreaShape_locoefa_coeff_46" "X048h_str_BF_AreaShape_locoefa_coeff_47"
[169] "X048h_str_BF_AreaShape_locoefa_coeff_48" "X048h_str_BF_AreaShape_locoefa_coeff_49"
[171] "X048h_str_BF_AreaShape_locoefa_coeff_5" "X048h_str_BF_AreaShape_locoefa_coeff_50"
[173] "X048h_str_BF_AreaShape_locoefa_coeff_51" "X048h_str_BF_AreaShape_locoefa_coeff_6"
[175] "X048h_str_BF_AreaShape_locoefa_coeff_7" "X048h_str_BF_AreaShape_locoefa_coeff_8"
[177] "X048h_str_BF_AreaShape_locoefa_coeff_9" "X048h_str_BF_AreaShape_major_axis_length"
[179] "X048h_str_BF_AreaShape_minor_axis_length" "X048h_str_BF_AreaShape_moments_hu_0"
[181] "X048h_str_BF_AreaShape_moments_hu_1" "X048h_str_BF_AreaShape_moments_hu_2"
[183] "X048h_str_BF_AreaShape_moments_hu_3" "X048h_str_BF_AreaShape_moments_hu_4"
[185] "X048h_str_BF_AreaShape_moments_hu_5" "X048h_str_BF_AreaShape_moments_hu_6"
[187] "X048h_str_BF_AreaShape_orientation" "X048h_str_BF_AreaShape_perimeter"
[189] "X072h_raw_BF_AreaShape_area" "X072h_raw_BF_AreaShape_aspect_ratio"
[191] "X072h_raw_BF_AreaShape_axis_major_length" "X072h_raw_BF_AreaShape_axis_minor_length"
[193] "X072h_raw_BF_AreaShape_eccentricity" "X072h_raw_BF_AreaShape_feret_diameter_max"
[195] "X072h_raw_BF_AreaShape_perimeter" "X072h_raw_BF_AreaShape_solidity"
[197] "X072h_raw_CH__bf_mask_Intensity_IntegratedIntensity" "X072h_raw_CH__bf_mask_Intensity_IntegratedIntensityEdge"
[199] "X072h_raw_CH__bf_mask_Intensity_LowerQuartileIntensity" "X072h_raw_CH__bf_mask_Intensity_MADIntensity"
[201] "X072h_raw_CH__bf_mask_Intensity_MassDisplacement" "X072h_raw_CH__bf_mask_Intensity_MaxIntensity"
[203] "X072h_raw_CH__bf_mask_Intensity_MaxIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_MeanIntensity"
[205] "X072h_raw_CH__bf_mask_Intensity_MeanIntensityEdge" "X072h_raw_CH__bf_mask_Intensity_MedianIntensity"
[207] "X072h_raw_CH__bf_mask_Intensity_MinIntensity" "X072h_raw_CH__bf_mask_Intensity_MinIntensityEdge"
[209] "X072h_raw_CH__bf_mask_Intensity_StdIntensity" "X072h_raw_CH__bf_mask_Intensity_StdIntensityEdge"
[211] "X072h_raw_CH__bf_mask_Intensity_UpperQuartileIntensity" "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_X"
[213] "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_Y" "X072h_raw_CH__bf_mask_Location_CenterMassIntensity_Z"
[215] "X072h_raw_CH__bf_mask_Location_Center_X" "X072h_raw_CH__bf_mask_Location_Center_Y"
[217] "X072h_raw_CH__bf_mask_Location_Center_Z" "X072h_raw_CH__bf_mask_Location_MaxIntensity_X"
[219] "X072h_raw_CH__bf_mask_Location_MaxIntensity_Y" "X072h_raw_CH__bf_mask_Location_MaxIntensity_Z"
[221] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_1of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_2of9"
[223] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_3of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_4of9"
[225] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_5of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_6of9"
[227] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_7of9" "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_8of9"
[229] "X072h_raw_CH__bf_mask_RadialDistribution_FracAtD_9of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_1of9"
[231] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_2of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_3of9"
[233] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_4of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_5of9"
[235] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_6of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_7of9"
[237] "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_8of9" "X072h_raw_CH__bf_mask_RadialDistribution_MeanFrac_9of9"
[239] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_1of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_2of9"
[241] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_3of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_4of9"
[243] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_5of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_6of9"
[245] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_7of9" "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_8of9"
[247] "X072h_raw_CH__bf_mask_RadialDistribution_RadialCV_9of9" "X072h_raw_CH_bra_mask_AreaShape_Area"
[249] "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxArea" "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_X"
[251] "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_Y" "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_X"
[253] "X072h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_Y" "X072h_raw_CH_bra_mask_AreaShape_Center_X"
[255] "X072h_raw_CH_bra_mask_AreaShape_Center_Y" "X072h_raw_CH_bra_mask_AreaShape_Compactness"
[257] "X072h_raw_CH_bra_mask_AreaShape_ConvexArea" "X072h_raw_CH_bra_mask_AreaShape_Eccentricity"
[259] "X072h_raw_CH_bra_mask_AreaShape_EquivalentDiameter" "X072h_raw_CH_bra_mask_AreaShape_EulerNumber"
[261] "X072h_raw_CH_bra_mask_AreaShape_Extent" "X072h_raw_CH_bra_mask_AreaShape_FormFactor"
[263] "X072h_raw_CH_bra_mask_AreaShape_MajorAxisLength" "X072h_raw_CH_bra_mask_AreaShape_MaxFeretDiameter"
[265] "X072h_raw_CH_bra_mask_AreaShape_MaximumRadius" "X072h_raw_CH_bra_mask_AreaShape_MeanRadius"
[267] "X072h_raw_CH_bra_mask_AreaShape_MedianRadius" "X072h_raw_CH_bra_mask_AreaShape_MinFeretDiameter"
[269] "X072h_raw_CH_bra_mask_AreaShape_MinorAxisLength" "X072h_raw_CH_bra_mask_AreaShape_Orientation"
[271] "X072h_raw_CH_bra_mask_AreaShape_Perimeter" "X072h_raw_CH_bra_mask_AreaShape_Solidity"
[273] "X072h_raw_CH_bra_mask_Intensity_IntegratedIntensity" "X072h_raw_CH_bra_mask_Intensity_IntegratedIntensityEdge"
[275] "X072h_raw_CH_bra_mask_Intensity_LowerQuartileIntensity" "X072h_raw_CH_bra_mask_Intensity_MADIntensity"
[277] "X072h_raw_CH_bra_mask_Intensity_MassDisplacement" "X072h_raw_CH_bra_mask_Intensity_MaxIntensity"
[279] "X072h_raw_CH_bra_mask_Intensity_MaxIntensityEdge" "X072h_raw_CH_bra_mask_Intensity_MeanIntensity"
[281] "X072h_raw_CH_bra_mask_Intensity_MeanIntensityEdge" "X072h_raw_CH_bra_mask_Intensity_MedianIntensity"
[283] "X072h_raw_CH_bra_mask_Intensity_MinIntensity" "X072h_raw_CH_bra_mask_Intensity_MinIntensityEdge"
[285] "X072h_raw_CH_bra_mask_Intensity_StdIntensity" "X072h_raw_CH_bra_mask_Intensity_StdIntensityEdge"
[287] "X072h_raw_CH_bra_mask_Intensity_UpperQuartileIntensity" "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_X"
[289] "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_Y" "X072h_raw_CH_bra_mask_Location_CenterMassIntensity_Z"
[291] "X072h_raw_CH_bra_mask_Location_Center_X" "X072h_raw_CH_bra_mask_Location_Center_Y"
[293] "X072h_raw_CH_bra_mask_Location_Center_Z" "X072h_raw_CH_bra_mask_Location_MaxIntensity_X"
[295] "X072h_raw_CH_bra_mask_Location_MaxIntensity_Y" "X072h_raw_CH_bra_mask_Location_MaxIntensity_Z"
[297] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_1of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_2of9"
[299] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_3of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_4of9"
[301] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_5of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_6of9"
[303] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_7of9" "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_8of9"
[305] "X072h_raw_CH_bra_mask_RadialDistribution_FracAtD_9of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_1of9"
[307] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_2of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_3of9"
[309] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_4of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_5of9"
[311] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_6of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_7of9"
[313] "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_8of9" "X072h_raw_CH_bra_mask_RadialDistribution_MeanFrac_9of9"
[315] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_1of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_2of9"
[317] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_3of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_4of9"
[319] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_5of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_6of9"
[321] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_7of9" "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_8of9"
[323] "X072h_raw_CH_bra_mask_RadialDistribution_RadialCV_9of9" "X072h_str_BF_AreaShape_area"
[325] "X072h_str_BF_AreaShape_aspect_ratio" "X072h_str_BF_AreaShape_eccentricity"
[327] "X072h_str_BF_AreaShape_equivalent_diameter" "X072h_str_BF_AreaShape_extent"
[329] "X072h_str_BF_AreaShape_form_factor" "X072h_str_BF_AreaShape_inertia_tensor_0_0"
[331] "X072h_str_BF_AreaShape_inertia_tensor_0_1" "X072h_str_BF_AreaShape_inertia_tensor_1_0"
[333] "X072h_str_BF_AreaShape_inertia_tensor_1_1" "X072h_str_BF_AreaShape_inertia_tensor_eigvals_0"
[335] "X072h_str_BF_AreaShape_inertia_tensor_eigvals_1" "X072h_str_BF_AreaShape_locoefa_PC_1"
[337] "X072h_str_BF_AreaShape_locoefa_PC_2" "X072h_str_BF_AreaShape_locoefa_PC_3"
[339] "X072h_str_BF_AreaShape_locoefa_PC_4" "X072h_str_BF_AreaShape_locoefa_PC_5"
[341] "X072h_str_BF_AreaShape_locoefa_UMAP_1" "X072h_str_BF_AreaShape_locoefa_UMAP_2"
[343] "X072h_str_BF_AreaShape_locoefa_UMAP_3" "X072h_str_BF_AreaShape_locoefa_coeff_0"
[345] "X072h_str_BF_AreaShape_locoefa_coeff_1" "X072h_str_BF_AreaShape_locoefa_coeff_10"
[347] "X072h_str_BF_AreaShape_locoefa_coeff_11" "X072h_str_BF_AreaShape_locoefa_coeff_12"
[349] "X072h_str_BF_AreaShape_locoefa_coeff_13" "X072h_str_BF_AreaShape_locoefa_coeff_14"
[351] "X072h_str_BF_AreaShape_locoefa_coeff_15" "X072h_str_BF_AreaShape_locoefa_coeff_16"
[353] "X072h_str_BF_AreaShape_locoefa_coeff_17" "X072h_str_BF_AreaShape_locoefa_coeff_18"
[355] "X072h_str_BF_AreaShape_locoefa_coeff_19" "X072h_str_BF_AreaShape_locoefa_coeff_2"
[357] "X072h_str_BF_AreaShape_locoefa_coeff_20" "X072h_str_BF_AreaShape_locoefa_coeff_21"
[359] "X072h_str_BF_AreaShape_locoefa_coeff_22" "X072h_str_BF_AreaShape_locoefa_coeff_23"
[361] "X072h_str_BF_AreaShape_locoefa_coeff_24" "X072h_str_BF_AreaShape_locoefa_coeff_25"
[363] "X072h_str_BF_AreaShape_locoefa_coeff_26" "X072h_str_BF_AreaShape_locoefa_coeff_27"
[365] "X072h_str_BF_AreaShape_locoefa_coeff_28" "X072h_str_BF_AreaShape_locoefa_coeff_29"
[367] "X072h_str_BF_AreaShape_locoefa_coeff_3" "X072h_str_BF_AreaShape_locoefa_coeff_30"
[369] "X072h_str_BF_AreaShape_locoefa_coeff_31" "X072h_str_BF_AreaShape_locoefa_coeff_32"
[371] "X072h_str_BF_AreaShape_locoefa_coeff_33" "X072h_str_BF_AreaShape_locoefa_coeff_34"
[373] "X072h_str_BF_AreaShape_locoefa_coeff_35" "X072h_str_BF_AreaShape_locoefa_coeff_36"
[375] "X072h_str_BF_AreaShape_locoefa_coeff_37" "X072h_str_BF_AreaShape_locoefa_coeff_38"
[377] "X072h_str_BF_AreaShape_locoefa_coeff_39" "X072h_str_BF_AreaShape_locoefa_coeff_4"
[379] "X072h_str_BF_AreaShape_locoefa_coeff_40" "X072h_str_BF_AreaShape_locoefa_coeff_41"
[381] "X072h_str_BF_AreaShape_locoefa_coeff_42" "X072h_str_BF_AreaShape_locoefa_coeff_43"
[383] "X072h_str_BF_AreaShape_locoefa_coeff_44" "X072h_str_BF_AreaShape_locoefa_coeff_45"
[385] "X072h_str_BF_AreaShape_locoefa_coeff_46" "X072h_str_BF_AreaShape_locoefa_coeff_47"
[387] "X072h_str_BF_AreaShape_locoefa_coeff_48" "X072h_str_BF_AreaShape_locoefa_coeff_49"
[389] "X072h_str_BF_AreaShape_locoefa_coeff_5" "X072h_str_BF_AreaShape_locoefa_coeff_50"
[391] "X072h_str_BF_AreaShape_locoefa_coeff_51" "X072h_str_BF_AreaShape_locoefa_coeff_6"
[393] "X072h_str_BF_AreaShape_locoefa_coeff_7" "X072h_str_BF_AreaShape_locoefa_coeff_8"
[395] "X072h_str_BF_AreaShape_locoefa_coeff_9" "X072h_str_BF_AreaShape_major_axis_length"
[397] "X072h_str_BF_AreaShape_minor_axis_length" "X072h_str_BF_AreaShape_moments_hu_0"
[399] "X072h_str_BF_AreaShape_moments_hu_1" "X072h_str_BF_AreaShape_moments_hu_2"
[401] "X072h_str_BF_AreaShape_moments_hu_3" "X072h_str_BF_AreaShape_moments_hu_4"
[403] "X072h_str_BF_AreaShape_moments_hu_5" "X072h_str_BF_AreaShape_moments_hu_6"
[405] "X072h_str_BF_AreaShape_orientation" "X072h_str_BF_AreaShape_perimeter"
[407] "X072h_str_CH_AreaShape_Bra_MajorAxis_Polarisation" "X072h_str_CH_AreaShape_Bra_MinorAxis_Polarisation"
[409] "X096h_raw_BF_AreaShape_area" "X096h_raw_BF_AreaShape_aspect_ratio"
[411] "X096h_raw_BF_AreaShape_axis_major_length" "X096h_raw_BF_AreaShape_axis_minor_length"
[413] "X096h_raw_BF_AreaShape_eccentricity" "X096h_raw_BF_AreaShape_feret_diameter_max"
[415] "X096h_raw_BF_AreaShape_perimeter" "X096h_raw_BF_AreaShape_solidity"
[417] "X096h_raw_CH_AreaShape_Bra_AreaFraction" "X096h_raw_CH__bf_mask_Intensity_IntegratedIntensity"
[419] "X096h_raw_CH__bf_mask_Intensity_IntegratedIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_LowerQuartileIntensity"
[421] "X096h_raw_CH__bf_mask_Intensity_MADIntensity" "X096h_raw_CH__bf_mask_Intensity_MassDisplacement"
[423] "X096h_raw_CH__bf_mask_Intensity_MaxIntensity" "X096h_raw_CH__bf_mask_Intensity_MaxIntensityEdge"
[425] "X096h_raw_CH__bf_mask_Intensity_MeanIntensity" "X096h_raw_CH__bf_mask_Intensity_MeanIntensityEdge"
[427] "X096h_raw_CH__bf_mask_Intensity_MedianIntensity" "X096h_raw_CH__bf_mask_Intensity_MinIntensity"
[429] "X096h_raw_CH__bf_mask_Intensity_MinIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_StdIntensity"
[431] "X096h_raw_CH__bf_mask_Intensity_StdIntensityEdge" "X096h_raw_CH__bf_mask_Intensity_UpperQuartileIntensity"
[433] "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_X" "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_Y"
[435] "X096h_raw_CH__bf_mask_Location_CenterMassIntensity_Z" "X096h_raw_CH__bf_mask_Location_Center_X"
[437] "X096h_raw_CH__bf_mask_Location_Center_Y" "X096h_raw_CH__bf_mask_Location_Center_Z"
[439] "X096h_raw_CH__bf_mask_Location_MaxIntensity_X" "X096h_raw_CH__bf_mask_Location_MaxIntensity_Y"
[441] "X096h_raw_CH__bf_mask_Location_MaxIntensity_Z" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_1of9"
[443] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_2of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_3of9"
[445] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_4of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_5of9"
[447] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_6of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_7of9"
[449] "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_8of9" "X096h_raw_CH__bf_mask_RadialDistribution_FracAtD_9of9"
[451] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_1of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_2of9"
[453] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_3of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_4of9"
[455] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_5of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_6of9"
[457] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_7of9" "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_8of9"
[459] "X096h_raw_CH__bf_mask_RadialDistribution_MeanFrac_9of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_1of9"
[461] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_2of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_3of9"
[463] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_4of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_5of9"
[465] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_6of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_7of9"
[467] "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_8of9" "X096h_raw_CH__bf_mask_RadialDistribution_RadialCV_9of9"
[469] "X096h_raw_CH_bra_mask_AreaShape_Area" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxArea"
[471] "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_X" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMaximum_Y"
[473] "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_X" "X096h_raw_CH_bra_mask_AreaShape_BoundingBoxMinimum_Y"
[475] "X096h_raw_CH_bra_mask_AreaShape_Center_X" "X096h_raw_CH_bra_mask_AreaShape_Center_Y"
[477] "X096h_raw_CH_bra_mask_AreaShape_Compactness" "X096h_raw_CH_bra_mask_AreaShape_ConvexArea"
[479] "X096h_raw_CH_bra_mask_AreaShape_Eccentricity" "X096h_raw_CH_bra_mask_AreaShape_EquivalentDiameter"
[481] "X096h_raw_CH_bra_mask_AreaShape_EulerNumber" "X096h_raw_CH_bra_mask_AreaShape_Extent"
[483] "X096h_raw_CH_bra_mask_AreaShape_FormFactor" "X096h_raw_CH_bra_mask_AreaShape_MajorAxisLength"
[485] "X096h_raw_CH_bra_mask_AreaShape_MaxFeretDiameter" "X096h_raw_CH_bra_mask_AreaShape_MaximumRadius"
[487] "X096h_raw_CH_bra_mask_AreaShape_MeanRadius" "X096h_raw_CH_bra_mask_AreaShape_MedianRadius"
[489] "X096h_raw_CH_bra_mask_AreaShape_MinFeretDiameter" "X096h_raw_CH_bra_mask_AreaShape_MinorAxisLength"
[491] "X096h_raw_CH_bra_mask_AreaShape_Orientation" "X096h_raw_CH_bra_mask_AreaShape_Perimeter"
[493] "X096h_raw_CH_bra_mask_AreaShape_Solidity" "X096h_raw_CH_bra_mask_Intensity_IntegratedIntensity"
[495] "X096h_raw_CH_bra_mask_Intensity_IntegratedIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_LowerQuartileIntensity"
[497] "X096h_raw_CH_bra_mask_Intensity_MADIntensity" "X096h_raw_CH_bra_mask_Intensity_MassDisplacement"
[499] "X096h_raw_CH_bra_mask_Intensity_MaxIntensity" "X096h_raw_CH_bra_mask_Intensity_MaxIntensityEdge"
[501] "X096h_raw_CH_bra_mask_Intensity_MeanIntensity" "X096h_raw_CH_bra_mask_Intensity_MeanIntensityEdge"
[503] "X096h_raw_CH_bra_mask_Intensity_MedianIntensity" "X096h_raw_CH_bra_mask_Intensity_MinIntensity"
[505] "X096h_raw_CH_bra_mask_Intensity_MinIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_StdIntensity"
[507] "X096h_raw_CH_bra_mask_Intensity_StdIntensityEdge" "X096h_raw_CH_bra_mask_Intensity_UpperQuartileIntensity"
[509] "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_X" "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_Y"
[511] "X096h_raw_CH_bra_mask_Location_CenterMassIntensity_Z" "X096h_raw_CH_bra_mask_Location_Center_X"
[513] "X096h_raw_CH_bra_mask_Location_Center_Y" "X096h_raw_CH_bra_mask_Location_Center_Z"
[515] "X096h_raw_CH_bra_mask_Location_MaxIntensity_X" "X096h_raw_CH_bra_mask_Location_MaxIntensity_Y"
[517] "X096h_raw_CH_bra_mask_Location_MaxIntensity_Z" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_1of9"
[519] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_2of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_3of9"
[521] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_4of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_5of9"
[523] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_6of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_7of9"
[525] "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_8of9" "X096h_raw_CH_bra_mask_RadialDistribution_FracAtD_9of9"
[527] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_1of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_2of9"
[529] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_3of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_4of9"
[531] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_5of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_6of9"
[533] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_7of9" "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_8of9"
[535] "X096h_raw_CH_bra_mask_RadialDistribution_MeanFrac_9of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_1of9"
[537] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_2of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_3of9"
[539] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_4of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_5of9"
[541] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_6of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_7of9"
[543] "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_8of9" "X096h_raw_CH_bra_mask_RadialDistribution_RadialCV_9of9"
[545] "X096h_str_BF_AreaShape_area" "X096h_str_BF_AreaShape_aspect_ratio"
[547] "X096h_str_BF_AreaShape_eccentricity" "X096h_str_BF_AreaShape_equivalent_diameter"
[549] "X096h_str_BF_AreaShape_extent" "X096h_str_BF_AreaShape_form_factor"
[551] "X096h_str_BF_AreaShape_inertia_tensor_0_0" "X096h_str_BF_AreaShape_inertia_tensor_0_1"
[553] "X096h_str_BF_AreaShape_inertia_tensor_1_0" "X096h_str_BF_AreaShape_inertia_tensor_1_1"
[555] "X096h_str_BF_AreaShape_inertia_tensor_eigvals_0" "X096h_str_BF_AreaShape_inertia_tensor_eigvals_1"
[557] "X096h_str_BF_AreaShape_locoefa_PC_1" "X096h_str_BF_AreaShape_locoefa_PC_2"
[559] "X096h_str_BF_AreaShape_locoefa_PC_3" "X096h_str_BF_AreaShape_locoefa_PC_4"
[561] "X096h_str_BF_AreaShape_locoefa_PC_5" "X096h_str_BF_AreaShape_locoefa_UMAP_1"
[563] "X096h_str_BF_AreaShape_locoefa_UMAP_2" "X096h_str_BF_AreaShape_locoefa_UMAP_3"
[565] "X096h_str_BF_AreaShape_locoefa_coeff_0" "X096h_str_BF_AreaShape_locoefa_coeff_1"
[567] "X096h_str_BF_AreaShape_locoefa_coeff_10" "X096h_str_BF_AreaShape_locoefa_coeff_11"
[569] "X096h_str_BF_AreaShape_locoefa_coeff_12" "X096h_str_BF_AreaShape_locoefa_coeff_13"
[571] "X096h_str_BF_AreaShape_locoefa_coeff_14" "X096h_str_BF_AreaShape_locoefa_coeff_15"
[573] "X096h_str_BF_AreaShape_locoefa_coeff_16" "X096h_str_BF_AreaShape_locoefa_coeff_17"
[575] "X096h_str_BF_AreaShape_locoefa_coeff_18" "X096h_str_BF_AreaShape_locoefa_coeff_19"
[577] "X096h_str_BF_AreaShape_locoefa_coeff_2" "X096h_str_BF_AreaShape_locoefa_coeff_20"
[579] "X096h_str_BF_AreaShape_locoefa_coeff_21" "X096h_str_BF_AreaShape_locoefa_coeff_22"
[581] "X096h_str_BF_AreaShape_locoefa_coeff_23" "X096h_str_BF_AreaShape_locoefa_coeff_24"
[583] "X096h_str_BF_AreaShape_locoefa_coeff_25" "X096h_str_BF_AreaShape_locoefa_coeff_26"
[585] "X096h_str_BF_AreaShape_locoefa_coeff_27" "X096h_str_BF_AreaShape_locoefa_coeff_28"
[587] "X096h_str_BF_AreaShape_locoefa_coeff_29" "X096h_str_BF_AreaShape_locoefa_coeff_3"
[589] "X096h_str_BF_AreaShape_locoefa_coeff_30" "X096h_str_BF_AreaShape_locoefa_coeff_31"
[591] "X096h_str_BF_AreaShape_locoefa_coeff_32" "X096h_str_BF_AreaShape_locoefa_coeff_33"
[593] "X096h_str_BF_AreaShape_locoefa_coeff_34" "X096h_str_BF_AreaShape_locoefa_coeff_35"
[595] "X096h_str_BF_AreaShape_locoefa_coeff_36" "X096h_str_BF_AreaShape_locoefa_coeff_37"
[597] "X096h_str_BF_AreaShape_locoefa_coeff_38" "X096h_str_BF_AreaShape_locoefa_coeff_39"
[599] "X096h_str_BF_AreaShape_locoefa_coeff_4" "X096h_str_BF_AreaShape_locoefa_coeff_40"
[601] "X096h_str_BF_AreaShape_locoefa_coeff_41" "X096h_str_BF_AreaShape_locoefa_coeff_42"
[603] "X096h_str_BF_AreaShape_locoefa_coeff_43" "X096h_str_BF_AreaShape_locoefa_coeff_44"
[605] "X096h_str_BF_AreaShape_locoefa_coeff_45" "X096h_str_BF_AreaShape_locoefa_coeff_46"
[607] "X096h_str_BF_AreaShape_locoefa_coeff_47" "X096h_str_BF_AreaShape_locoefa_coeff_48"
[609] "X096h_str_BF_AreaShape_locoefa_coeff_49" "X096h_str_BF_AreaShape_locoefa_coeff_5"
[611] "X096h_str_BF_AreaShape_locoefa_coeff_50" "X096h_str_BF_AreaShape_locoefa_coeff_51"
[613] "X096h_str_BF_AreaShape_locoefa_coeff_6" "X096h_str_BF_AreaShape_locoefa_coeff_7"
[615] "X096h_str_BF_AreaShape_locoefa_coeff_8" "X096h_str_BF_AreaShape_locoefa_coeff_9"
[617] "X096h_str_BF_AreaShape_major_axis_length" "X096h_str_BF_AreaShape_minor_axis_length"
[619] "X096h_str_BF_AreaShape_moments_hu_0" "X096h_str_BF_AreaShape_moments_hu_1"
[621] "X096h_str_BF_AreaShape_moments_hu_2" "X096h_str_BF_AreaShape_moments_hu_3"
[623] "X096h_str_BF_AreaShape_moments_hu_4" "X096h_str_BF_AreaShape_moments_hu_5"
[625] "X096h_str_BF_AreaShape_moments_hu_6" "X096h_str_BF_AreaShape_orientation"
[627] "X096h_str_BF_AreaShape_perimeter" "X096h_str_CH_AreaShape_Bra_MajorAxis_Polarisation"
[629] "X096h_str_CH_AreaShape_Bra_MinorAxis_Polarisation"
Now we can save this monstrosity to disc:
saveRDS(Gastruloid_48h_merged_afterQC, file = "df48v3_updated_morphodata.rds")